I'm still not totally clear on what it is you're trying to accomplish, but if what you want is to cut the quill down a bit, that's not a problem at all. Just do it. I've done that with no problem, and with only a hacksaw and nothing to clamp it down with but my hands. You can easily even it out with a file afterwards if you need to, although if you can, some means of clamping down the stem and controlling the angle of the cut would be easier. Me, I just used the wedge itself as a guide to make a mark on the quill.

As long as you end up being able to put 2 and half inches of stem into the tube, you should be fine. I disagree with others that having more quill sticking up out of the tube in relation to the shorter length in the tube is going to affect safety. It won't if you have those 2 and half inches in there. That's all you need. Less, and you're on your own. That 2 and half inches I'm talking about includes right down to the very bottom point of the quill.

By the way, on a classic style bike, a slightly cut down Technomic Deluxe that isn't sticking a mile up from the head tube looks absolutely terrific. It has that classic drop down nose that many of us love. I have some 3TTT Synthesis stems for my custom-made lugged frame, but I actually prefer the Technomic on it just for the looks. I took about an inch off the quill because it was bottoming out too early. It was actually the guys at Rivendell who suggested cutting it. They probably don't get too many calls about a Technomic being too long :-)